This description relates to chemical array chips, particularly biochemical arrays, used for chemical analysis by optical techniques.
Array chips, such as those used in chemical and biochemical assays, allow large numbers of biochemical experiments to be performed in parallel. For example, a biochemical array chip may be part of a system for processing biochemical experiments in parallel. Array chips have solid, planar substrates made from silicon or glass wafers, or other materials. Biomolecules, reagents, fluorescent markers and other chemical compounds are applied to array chips in regular patterns.
Biochemical experiments may be performed on array chips by washing reagents over them according to precise protocols that specify chemical compounds and mixtures to be used, temperature, incubation time, and other parameters appropriate to a particular type of experiment.
In some operational contexts, biochemical experiments may be used along with fluorescence imaging to identify DNA bases—A, C, G, or T—by designing biochemical reactions such that a different colored dye (for example, red, green, blue, or yellow) corresponds to each one. For example, a fluorescence microscope or other suitable optical system may be used to take images of the biochemical experiments disposed and/or conducted on an array chip. The colors observed indicate the DNA bases at that particular experiment step. Extracting data from an array chip with such DNA experiments thus depends on recording the color of fluorescence emitted by many millions or even billions of biochemical experiments that may be present on the chip.
However, obtaining useful data from a fluorescence image of a dense biochemical array chip is complicated by competing interests of spatial resolution, accuracy, and speed. Images must be obtained at high enough magnification for individual experiments to be clearly resolved. At the same time images must cover a large enough field of view for experiments to be correctly identified. Finally, for large scale studies, imaging and image processing must take place quickly enough to provide for sufficient throughput and to make sequencing operations commercially feasible.